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The Flux Simulator uses a 3-step algorithm to tokenize a molecule; first, geometry and the number of fragments that are obtained from the molecule are determined. We found empirically that parameter d depends logarithmically on , the length of the molecule that is fragmented . The number of fragments produced from a specific RNA molecule is determined by , where is the expectancy of the most abundant fragment size, computed from h and the gamma-function of :
Second, breakpoints are sampled uniformly from the interval [0;1[, resulting in relative length fractions for all all fragments. Third, relative fragment sizes are transformed from unit space to sizes that follow a Weibull distribution of shape d shape by:
where is a constant of the transformation to ensure that the sizes of the fragments sum up exactly to the given molecule length. Latter transformation produces a slightly distorted Weibull distribution for the sizes , however the deviation is sufficiently small to be neglected in our applications.